For characters that use flurry w/ unarmed, there is no need to "arm" both hands. (Or either hand, IIRC). HeroLab handles them as separate things because flurrying is not done with a primary hand and an off hand. It's done with hands, elbows, knees, head, feet - pick your flavor.

You check the "Flurry" box on the "In Play" tab, and it adds the extra attack to the character.